Ontology highlight
ABSTRACT:
PROVIDER: PRJNA914524 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22853700_1.fastq.gz | Fastqsanger.gz | |||
| SRR22853700_2.fastq.gz | Fastqsanger.gz | |||
| SRR22853800_1.fastq.gz | Fastqsanger.gz | |||
| SRR22853800_2.fastq.gz | Fastqsanger.gz | |||
| SRR22853900_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 428 |
Similar Datasets
Project description:Autism spectrum disorder (ASD) is a heterogenous neurodevelopmental disorder with complex pathophysiology including both genetic and environmental factors. Recent evidence demonstrates the gut microbiome and its resultant metabolome can influence brain and behavior and have been implicated in ASD. To investigate gene by microbiome interactions in a model for genetic risk of ASD, we utilize mutant mice carrying a deletion of the ASD-associated Shank3 gene (Shank3KO). Shank3KO have altered microbiome composition and function at baseline in addition to social deficits. Further depletion of the microbiome with antibiotics exacerbates social deficits in Shank3KO, and results in transcriptional changes in the frontal cortex. Supplementation with the microbial metabolite acetate leads to reversal of social behavioral phenotypes even in mice with a depleted microbiome, and significantly alters transcriptional regulation in the prefrontal cortex. These results suggest a key role for the gut microbiome and the neuroactive metabolite acetate in regulating ASD-like behaviors.
2023-03-02 | GSE225983 | GEO
Project description:Tissue specific transcriptomics of social spider Stegodyphus dumicola
| PRJNA575239 | ENA
Project description:Single-brain transcriptomics of a social spider Stegodyphus dumicola
| PRJNA781012 | ENA
Project description:Social interactions are typically characterised by conflict and competition. This antagonism can play a critical role in evolutionary processes, such as promoting diversity through maintenance of alternative strategies or driving accelerated evolution through arms-race like escalation. However, despite our sophisticated understanding of how conflict shapes social traits, we still have limited knowledge of how it impacts molecular evolution across the underlying ‘social genes’. To address this problem, we analysed the genome wide impact of social interactions in a microbe. To understand broad-scale processes shaping molecular evolution at social genes we have used four different, but complementary, approaches to identify sets of social genes. For ease, we have named these sets ‘sociality’, ‘chimerism’, ‘antagonism’ and ‘cheater’ genes. Chimerism genes are defined as those up-regulated in chimeric aggregations in comparison to clonal aggregations. This is based on the logic that chimeric development will be characterised by conflict, and hence these genes will show the signatures of conflict driven evolution. Using genome sequences from 67 Dictyostelium discoideum strains, we find that social genes often exhibit enhanced polymorphism and accelerated evolution. However, these patterns are not consistent with the expectation of conflict driven processes, but instead reflect relatively relaxed purifying selection. This pattern reflects the fact that social interactions are conditional, and therefore selection on genes expressed in social interactions is diluted by generations of inactivity. This results in the ‘Red King’ process, wherein dilution of selection by inactivity enhances the role of drift, resulting in increased polymorphism and accelerated evolution.
2019-05-09 | GSE118081 | GEO
Project description:Spiders are a highly diverse group of arthropods that occur in most habitats on land. Notably, spiders have significant ecological impact as predators because of their extraordinary prey capture adaptations, venom and silk. Spider venom is among the most heterogeneous animal venoms and has pharmacological applications, while spider silk is characterized by great toughness with potential for biomaterial application. We describe the genome sequences of two spiders representing two major taxonomic groups, the social velvet spider Stegodyphus mimosarum (Araneomorphae), and the Brazilian white-knee tarantula Acanthoscurria geniculata (Mygalomorphae). We annotate genes using a combination of transcriptomic and in-depth proteomic analyses. The genomes are large (2.6 Gb and 6 Gb, respectively) with short exons and long introns and approximately 50% repeats, reminiscent of typical mammalian genomes. Phylogenetic analyses show that spiders and ticks are sister groups outgrouped by mites, and phylogenetic dating using a molecular clock dates separation of velvet spider and tarantula at 270 my. Based on the genomes and proteomes, we characterize the genetic basis of venom and silk production of both species in detail. Venom protein composition differs markedly between the two spiders, with lipases as the most abundant protein in the velvet spider and present only at low concentration in tarantula. Venom in both spiders contains proteolytic enzymes, and our analyses suggest that these enzymes target and process precursor peptides that subsequently mediate the toxic effects of venom. Complete analysis of silk genes reveal a diverse suite of silk proteins in the velvet spider including novel types of spidroins, and dynamic evolution of major ampullate spidroin genes, whereas silk protein diversity in tarantula is far less complex. The difference in silk proteins between species is consistent with a more complex silk gland morpholgy and use of three-dimentional capture webs consisting of multiple silk types in aranomorph spiders.
2014-05-01 | PXD000318 | Pride
Project description:Our analysis reveals an extensive methylomic drift between normal squamous esophagus and BE tissues in nonprogressed BE patients, with differential drift affecting 4024 (24%) of 16,984 normally hypomethylated cytosine-guanine dinucleotides (CpGs) occurring in CpG islands. The majority (63%) of islands that include drift CpGs are associated with gene promoter regions. Island CpGs that drift have stronger pairwise correlations than static islands, reflecting collective drift consistent with processive DNA methylation maintenance. Individual BE tissues are extremely heterogeneous in their distribution of methylomic drift and encompass unimodal low-drift to bimodal high-drift patterns, reflective of differences in BE tissue age. Further analysis of longitudinally collected biopsy samples from 20 BE patients confirm the time-dependent evolution of these drift patterns. Drift patterns in EAC are similar to those in BE, but frequently exhibit enhanced bimodality and advanced mode drift. To better understand the observed drift patterns, we developed a multicellular stochastic model at the CpG island level. Importantly, we find that nonlinear feedback in the model between mean island methylation and CpG methylation rates is able to explain the widely heterogeneous collective drift patterns. Using matched gene expression and DNA methylation data in EAC from TCGA and other publically available data, we also find that advanced methylomic drift is correlated with significant transcriptional repression of ~ 200 genes in important regulatory and developmental pathways, including several checkpoint and tumor suppressor-like genes. Taken together, our findings suggest that epigenetic drift evolution acts to significantly reduce the expression of developmental genes that may alter tissue characteristics and improve functional adaptation during BE and EAC progression.
2017-10-31 | GSE104707 | GEO
Project description:Social behaviour is regulated by activity of host-associated microbiota across multiple species. However, the molecular mechanisms mediating this relationship remain elusive. We therefore determined the dynamic, stimulus-dependent transcriptional regulation of germ-free (GF) and GF mice colonised post weaning (exGF) in the amygdala, a brain region critically involved in regulating social interaction. In GF mice the dynamic response seen in controls was attenuated and replaced by a marked increase in expression of splicing factors and alternative exon usage in GF mice upon stimulation, which was even more pronounced in exGF mice. In conclusion, we demonstrate a molecular basis for how the host microbiome is crucial for a normal behavioural response during social interaction. Our data further suggest that social behaviour is correlated with the gene-expression response in the amygdala, established during neurodevelopment as a result of host-microbe interactions. Our findings may help toward understanding neurodevelopmental events leading to social behaviour dysregulation.
2018-05-23 | GSE114702 | GEO
Project description:The common house spider Parasteatoda tepidariorum is a chelicerate model organism for studying developmental mechanisms and their evolution in arthropods. In contrast to the well-studied model insect, Drosophila melanogaster, embryos of the spider undergo patterning in a cellular environment from early stages (at least after the number of the nuclei increase to 16). Use of spider embryos provide new opportunities to understand the evolution of developmental mechanisms underlying arthropod body plans. This analysis aims to generate genome-scale, developmental profiles of gene expression in embryos of the spider P. tepidariorum, which facilitate a wide range of studies using this spider species.
2018-04-05 | GSE112712 | GEO